结核分枝杆菌PhoPR双组分系统与不同毒力结核分枝杆菌致病性的相关性研究

目的：通过比较分析卡介苗株（BCG）、结核分枝杆菌国际标准无毒株（H37Ra）、结核分枝杆菌国际标准强毒株（ H37Rv）、新疆地区流行的优势强毒株结核分枝杆菌临床分离株（ XJ-MTB）的PhoP基因和PhoR基因的表达水平差异,探讨研究结核分枝杆菌PhoPR双组分系统与不同毒力结核分枝杆菌的致病性是否具有相关性。方法：首先提取上述四种不同毒力结核分枝杆菌菌株的总RNA,并进行完整性鉴定;再运用SYBR Green I实时荧光定量PCR技术检测各组菌株中PhoP基因和PhoR基因的表达水平;最后比较不同毒力结核分枝杆菌PhoP基因和PhoR基因的表达水平差异。结果：四种不同毒力菌株PhoP基因的相对表达量,由高到低依次为XJ-MTB（9.05）、H37Rv（1.00）、H37Ra（0.25）、BCG（0.08）,且四种菌株中PhoP基因的表达有显著的统计学差异（P＜0.05）;同时四种不同毒力菌株PhoR基因的相对表达量,由高到低依次为XJ-MTB（5.72）、H37Rv（1.00）、H37Ra（0.18）、BCG（0.07）,且四种菌株中PhoR基因的表达有显著的统计学差异（P＜0.05）。其中XJ-MTB菌株PhoP基因和PhoR基因的表达水平与BCG、H37Rv、H37Ra相比存在显著的统计学差异（P＜0.05）;H37Rv菌株PhoP基因和PhoR基因的表达与BCG、H37Ra相比存在显著的统计学差异（P＜0.05）;而BCG菌株PhoP基因和PhoR基因的表达与H37Ra相比统计学差异不显著（ P＞0.05）。结论：结核分枝杆菌PhoPR双组分系统中PhoP基因和PhoR基因在不同毒力结核分枝杆菌中的表达存在差异,并且该系统与不同毒力结核分枝杆菌的致病性存在相关性。     

大鼠肝细胞热适应差异表达基因消减文库的构建与鉴定

目的: 构建大鼠肝细胞热适应差异表达基因消减文库。方法: 实验采用热适应大鼠模型、常温对照。提取肝组织mRNA,反转录cDNA并酶切、接头连接后分别以其中一组cDNA片段为tester, 另一组为driver进行抑制性消减杂交(SSH)构建消减文库。PCR扩增文库和未消减对照样品中的G3PDH基因以对比评估文库特异性。初步分离、筛选以评估文库的可靠性。结果: PCR证实文库中G3PDH丰度大幅低于对照组,说明文库特异性较高。从文库中分离获得300个目的基因片段, 其中27个经鉴定为差异表达基因, 证实文库高效可靠。结论: 通过构建优质的热适应差异表达基因消减文库, 为深入研究热适应机理奠定了基础。     

结核分枝杆菌Ag85A蛋白的原核表达、纯化和免疫反应性

目的通过原核表达获得结核分枝杆菌Ag85A蛋白。方法用PCR从结核分枝杆菌H37Rv菌株中扩增出编码Ag85A的fbpA基因,克隆入原核表达载体pProEXHTb,产生重组质粒pPro85A后,转化至大肠杆菌感受态细胞BL21并诱导大量表达。用镍纯化系统纯化重组Ag85A蛋白,用不同分枝杆菌感染的小鼠血清通过ELISA确定其免疫反应性。利用PCR技术鉴定fbpA基因在不同分枝杆菌的分布。结果32 ku的Ag85A蛋白获得高效表达和纯化。表达Ag85A蛋白的fbpA基因在结核分枝杆菌H37Rv、H37Ra、BCG、草分枝杆菌、土地分枝杆菌、耻垢分枝杆菌和次要分枝杆菌中均有表达,但在牝牛分枝杆菌中未表达。结核病患者和结核分枝杆菌毒株H37Rv感染小鼠血清所产生的抗Ag85A抗体滴度最高。结论重组Ag85A蛋白已成功表达纯化,并保留了免疫反应性。     

抑制性消减杂交技术筛选重组IFNβ下调HepG2细胞靶基因

目的利用抑制性消减杂交（SSH）技术构建重组干扰素β（IFNβ）刺激人肝癌细胞系HepG2差异表达基因的cDNA消减文库，筛选IFNβ下凋HepG2相关基因。方法重组IFNβ2000U／ml刺激对数生长期HepG2细胞，以生理盐水作用的HepG2细胞为阴性对照；制备细胞裂解液，从中提取mRNA并逆转录为cDNA，经Rsa Ⅰ酶切后将实验组cDNA分成两份，分别与两种不同的接头连接，再与对照组cDNA进行两次消减杂交及两次抑制性PCR，将产物与T／A载体连接，构建cDNA消减文库，并转染大肠埃希菌进行文库扩增，随机挑选克隆PCR后进行测序及同源性分析。结果成功构建重组IFNβ刺激HepG2细胞差异表达基因的cDNA消减文库。文库扩增后，得到58个阳性克隆，进行菌落PCR分析，均得到200～1000bp插入片段。随机挑选其中35个插入片段测序，并通过生物信息学分析，结果共获得12种编码基因。结论应用SSH技术成功构建了IFNβ刺激HepG2细胞差异表达基因的cDNA消减文库，为进一步了解IFNβ在肝细胞内的免疫调节机制提供了依据。     

构建不稳定型心绞痛淋巴细胞差异表达cDNA消减文库

目的:构建不稳定型心绞痛淋巴细胞差异表达cDNA消减文库。方法:将不稳定型心绞痛病人(n=15)和稳定型心绞痛病人(n=15)的淋巴细胞的RNA进行抑制性消减杂交(SSH), 将获得的顺向和逆向消减产物分别与T/A载体连接, 采用1×TSS一步法转化大肠杆菌JM109, 获得消减cDNA文库, 采用蓝白斑筛选和菌落PCR筛选有插入片段的克隆。结果:各组cDNA文库各获得2000个阳性克隆, cDNA片段大部分分布于(200-600)bp之间。结论:本研究构建了不稳定型心绞痛淋巴细胞消减cDNA文库, 此cDNA文库有助于进一步筛选不稳定型心绞痛淋巴细胞中的差异表达基因。     

IgA肾病肾阴虚证cDNA文库的构建

目的应用抑制性消减杂交（suppression subtractive hybridization,SSH）技术构建汉族人IgA肾病肾阴虚证cDNA消减文库。方法选择IgA肾病且中医辨证为肾阴虚证的患者以及正常人作为其对照组,进行正向和反向消减杂交。采用Trizol BD法提取总RNA,用SMART技术逆转录并扩增总cDNA,用RsaⅠ酶切基因组cDNA成大小不等的片段,分别与两种不同的接头连接,进行2次消减杂交及2次抑制性PCR,然后将PCR产物与U载体连接,经蓝白斑筛选后,再用PCR方法插入片段筛选出阳性重组质粒,构建IgA肾病肾阴虚证消减文库。结果用SSH方法筛选出了IgA肾病肾阴虚证的差异cDNA片段,其中正向消减文库共获得325个阳性克隆．反向消减文库获得306个阳性克隆,从而成功地构建了IgA肾病肾阴虚证的cDNA消减文库。结论SSH技术能够快速有效地分离差异cDNA片段,成功构建了IgA肾病肾阴虚证的cDNA文库,为进一步克隆肾阴虚证的相关基因奠定了基础。     

胃癌下调基因组cDNA抑制消减文库的建立及鉴定

目的 建立胃癌下调基因组cDNA抑制消减文库并鉴定。方法 采用高灵敏度的抑制消减杂交技术，建立五人份正常胃粘膜mRNA(Tester)抑制消减杂交胃癌mRNA(Driver)的差异表达文库，用PCR及差异表达克隆菌转膜反向杂交判定其消减效率。结果 所构建胃癌下调基因抑制消减杂交cDNA文库，消减效率高，胃癌下调基因在正常胃粘膜及胃癌组织中的差异表达符合率达86％。结论 成功建立了用于筛选胃癌下调基因的抑制消减杂交cDNA文库。     

采用基因打靶技术构建结核分枝杆菌新基因Rv0901缺失株的研究

目的：利用基因打靶技术构建基因打靶载体和基因缺失株，用于结核分枝杆菌基因Rv0901功能的研究。方法：结核分枝杆菌标准株H37Rv体外培养，对其Rv0901基因及两侧序列进行体外扩增，连接载体及目的片段，切除目的基因，再引入筛选标志构建重组自杀质粒，分别用酶切及PCR鉴定；用电穿孔法将重组自杀质粒转入结核杆菌H37Rv株，用PCR鉴定。结果：经鉴定PCR产物及插入片段大小与预期值相符，且为所需目的基因片段，成功切除靶片段；蓝白斑筛选证实标记基因插入片段插入方向正确；Rv0901基因缺失株用PCR鉴定成功缺失了目的基因片段2.5 kb。结论：成功构建了用于结核分枝杆菌基因打靶的置换型载体和Rv0901新基因缺失株，为Rv0901基因功能的研究奠定了基础。     

靶向沉默Mcl-1基因对感染不同毒力结核杆菌小鼠腹腔巨噬细胞凋亡的影响

 目的: 通过RNA干扰技术特异性沉默 Mcl-1 基因,探讨下调 Mcl-1 基因对感染不同毒力结核杆菌小鼠腹腔巨噬细胞凋亡的影响。方法: 分别用制备好的新疆地区流行的优势强毒结核分枝杆菌临床分离株(简称强毒株)、结核分枝杆菌国际标准强毒株H37Rv(简称H37Rv)、结核分枝杆菌国际标准无毒株H37Ra(简称H37Ra)和卡介苗(BCG)菌悬液感染BALB/c小鼠,再以筛选并构建好的Mcl-1-shRNA作用于感染的小鼠模型,同时设立相应对照组,于作用后1 d、3 d、5 d和7 d提取小鼠腹腔巨噬细胞,应用实时荧光定量PCR和Western blot检测各组小鼠腹腔巨噬细胞中Mcl-1 mRNA和蛋白的表达;应用流式细胞术检测各组巨噬细胞的凋亡水平。结果: 小鼠被不同毒力的结核杆菌感染后其腹腔巨噬细胞中Mcl-1 mRNA和蛋白的表达水平均有不同程度的升高,其中以感染了强毒株和H37Rv的腹腔巨噬细胞升高最为明显(P<0.05);应用RNA干扰技术沉默 Mcl-1 基因后,Mcl-1 mRNA和蛋白的表达水平明显低于对照组(P<0.05);流式细胞术分析显示,下调 Mcl-1 基因的表达可诱导小鼠腹腔巨噬细胞凋亡。结论: 应用Mcl-1-shRNA可有效沉默 Mcl-1 在感染了不同毒力结核杆菌小鼠腹腔巨噬细胞中的表达,并能上调巨噬细胞的凋亡水平。     

结核分枝杆菌PPE15蛋白的原核表达、鉴定及其兔多克隆抗体的制备

目的 克隆、表达和纯化结核分枝杆菌脯氨酸-脯氨酸-谷氨酸15(PPE15)蛋白,制备并鉴定PPE15蛋白兔多克隆抗体.方法 通过PCR从结核分枝杆菌H37Rv株基因组扩增PPE15基因,利用同源重组克隆技术构建原核表达组氨酸标签PPE15蛋白的pET28a-PPE15载体.将pET28a-PPE15转化至大肠杆菌BL2...     

应用抑制性消减杂交技术筛选结核分枝杆菌差异基因

目的 筛选新疆地区结核分枝杆菌临床分离株与国际标准株H37Rv之间的差异基因,初步分析这些基因的功能.方法 利用抑制性消减杂交技术,通过两轮两相杂交,驱赶相同基因富集差异基因.结果 正相抑制性消减杂交一共获得6条新疆地区临床分离株中存在的差异基因,虽然这些基因在H37Rv基因组中不存在,但与国际标准临床株CDC1551以及复合群国际标准株KMS中的对应基因高度同源,分别与编码多萜醇磷酸甘露糖基转移酶Ⅱ、单加氧酶黄素结合蛋白、酰基转移酶蛋白、染色体复制起始密码子、脂酰基载体蛋白以及5'-磷酸吡哆胺氧化酶的基因有关.结论 新疆地区结核分枝杆菌临床分离株与国际标准株H37Rv之间存在差异基因,这些差异基因的功能可能与已知同源基因的功能相似:增强细菌胞壁蛋白的吸附能力、抵抗氮氧合酶消化、提高乙酰基辅酶A的合成能力、调控复制起始密码子、合成胞壁脂酰基载脂蛋白和促进5'-磷酸吡哆胺氧化酶代谢.     

Genomic Analysis Reveals Variation between Mycobacterium tuberculosis H37Rv and the Attenuated M. tuberculosis H37Ra Strain

Mycobacterium tuberculosis H37Ra is an attenuated tubercle bacillus closely related to the virulent type strain M. tuberculosis H37Rv. Despite extensive study, the reason for the decreased virulence of M. tuberculosis H37Ra has not been determined. A genomic approach was therefore initiated to identify genetic differences between M. tuberculosis H37Rv and M. tuberculosis H37Ra as a means of pinpointing the attenuating mutation(s). Digestion with the rare-cutting restriction endonuclease DraI revealed two polymorphisms between the strains: a 480-kb fragment in M. tuberculosis H37Rv was replaced by two fragments of 220 and 260 kb in M. tuberculosis H37Ra, while there was a approximately 7.9-kb DraI fragment in M. tuberculosis H37Ra that had no counterpart in M. tuberculosis H37Rv. As the M. tuberculosis insertion sequence IS6110 contains a single DraI restriction site, it was considered possible that these polymorphisms were the result of IS6110 transposition events in M. tuberculosis H37Ra, events that may have inactivated virulence genes. The 7.9-kb polymorphism was found to be due to the presence of the previously described H37Rv RvD2 deletion in M. tuberculosis H37Ra, with sequence analysis suggesting an IS6110-mediated deletion mechanism for loss of RvD2. Three other IS6110-catalyzed deletions from the M. tuberculosis H37Rv chromosome (RvD3 to RvD5) were also identified, suggesting that this mechanism plays an important role in genome plasticity in the tubercle bacilli. Comparative mapping and sequencing revealed that the 480-kb polymorphism was due to an IS6110 insertion in M. tuberculosis H37Ra near oriC. Complementation of M. tuberculosis H37Ra with a 2.9-kb restriction fragment from M. tuberculosis H37Rv that encompassed the IS6110 insertion did not increase the survival of recombinant M. tuberculosis H37Ra in mice. In conclusion, this study describes the presence and mechanisms of genomic variation between M. tuberculosis H37Ra and M. tuberculosis H37Rv, although the role that they play in the attenuation of M. tuberculosis H37Ra is unclear.     

Expression of contact-dependent cytolytic activity by Mycobacterium tuberculosis and isolation of the genomic locus that encodes the activity.

We investigated the presence of cytolytic activity in the virulent H37Rv and attenuated H37Ra strains of Mycobacterium tuberculosis and in the vaccine strain Mycobacterium bovis BCG. The virulent strain H37Rv expressed > 3-fold more contact-dependent cytolytic activity than the attenuated strain H37Ra, and the vaccine strain M. bovis BCG did not produce cytolytic activity. We also isolated an approximately 3.2-kbp fragment of the M. tuberculosis H37Rv genome that was capable of inducing this contact-dependent hemolytic activity in a nonhemolytic strain of Escherichia coli.     

Human alveolar macrophage gene responses to Mycobacterium tuberculosis strains H37Ra and H37Rv

H37Rv and H37Ra have been widely used as models of virulent and avirulent strains, respectively, of Mycobacterium tuberculosis. Since the sequencing of H37Rv, microarrays have been used to investigate gene expression of M. tuberculosis strains under various conditions, and to compare gene expression of specific isolates of the organism. Because differences in the virulence of these organisms could also be manifest via their differential induction of host genes, we used Affymetrix Human Genome Arrays U133A and U133B to evaluate human alveolar macrophage (AM) responses to infection with H37Rv and H37Ra. H37Rv altered expression of far more genes than did H37Ra. Moreover, the genes induced by H37Rv to a greater extent than by H37Ra were predominantly associated with the development of effective immunity. H37Rv markedly increased expression of IL-23 p19, whereas neither organism significantly induced IL-12 p35 expression. Quantitative PCR confirmed that H37Rv induced significantly more AM p19 expression than did H37Ra. After low-level infection of both AM and peripheral blood monocytes (MN) with H37Rv, neither cell type produced IL-12 (by ELISA). In contrast, AM displayed significant IL-23 production in response to H37Rv, whereas MN did not. Our findings thus suggest an important role for IL-23 in human host responses to pulmonary infection with M. tuberculosis, and are consistent with epidemiologic and genetic studies that imply that H37Rv may not have unusual capacity to cause human disease.     

Use of in vivo complementation in Mycobacterium tuberculosis to identify a genomic fragment associated with virulence.

Novel molecular tools and genetic methods were developed to isolate genomic fragments of Mycobacterium tuberculosis that may be associated with virulence. We sought to restore virulence, a characteristic of M. tuberculosis that is correlated with growth rate in mouse spleen and lung tissue, to the avirulent strain H37Ra by complementation. A representative library of the virulent M. tuberculosis strain H37Rv was constructed and transformed into H37Ra. Enrichment for individual faster-growing recombinants was achieved by passage of pools of H37Ra transformants harboring the H37Rv library through mice. A molecular strategy was devised to isolate and clone the H37Rv genomic DNA fragment ivg, which conferred a more rapid in vivo growth rate to H37Ra.     

Pathogenesis of tuberculosis: interaction of Mycobacterium tuberculosis with macrophages.

Central to understanding the pathogenesis of tuberculosis is the interaction between the pathogen and mononuclear phagocytes. A key question about that interaction is whether Mycobacterium tuberculosis exerts an effect on phagolysosome fusion. We have reexamined the dynamics of phagolysosome fusion and its effect on intracellular bacterial replication in M. tuberculosis-infected macrophages by performing an extensive study at the electron microscopic level. Thoria-labelled murine and human macrophages were infected with a virulent (H37Rv) or avirulent (H37Ra) strain of M. tuberculosis or with Mycobacterium bovis BCG vaccine for times ranging from 2 h to 7 days. In all cases, by 2 h postinfection, approximately 85% of the bacteria clearly resided in fused vacuoles. However, at 4 days postinfection, fusion levels for viable H37Rv and H37Ra were reduced by half, whereas the fusion profiles of BCG and of heat-killed H37Rv and H37Ra were unchanged. A comparison of the numbers of bacteria per fused and nonfused vacuoles suggests both a net transfer of bacteria out of fused vacuoles and preferential bacterial multiplication in nonfused vacuoles. H37Rv and H37Ra appeared to bud from the phagolysosomes into tightly apposed membrane vesicles that did not fuse with secondary lysosomes. In some cases, no such membrane was seen and the bacteria appeared to be free in the cytoplasm. Only viable H37Rv showed a significant increase in bacterial counts during the course of infection. Thus, both of the attenuated strains we examined differed from the virulent strain H37Rv in their abilities to replicate successfully within macrophages, but each diverged from H37Rv at a different point in the process. Viable tubercle bacilli H37Rv and H37Ra had the capacity to escape from fused vesicles as the infection progressed; BCG did not. After extrusion from the phagolysosome, H37Rv, but not H37Ra, was able to multiply. These results suggest a novel mechanism by which virulent M. tuberculosis eludes the microbicidal mechanisms of macrophages by escaping from fused phagolysosomes into nonfused vesicles or the cytoplasm.     

IS6110-based restriction fragment length polymorphism (RFLP) analysis of Mycobacterium tuberculosis H37Rv and H37Ra

IS6110-based restriction fragment length polymorphism (RFLP) analysis of Mycobacterium tuberculosis H37Rv and its avirulent mutant H37Ra was performed by a number of restriction enzymes, including Nru I, EcoN I, Pst I, and Pvu II. No differences were found in the IS 6110-fingerprints of the study strains by Nru I. One differential IS6110-positive restriction fragment was detected by EcoN I in strain H37Ra, while analysis by Pst I revealed that two fragments of the strain H37Rv were replaced by four novel IS6110-positive fragments in the strain H37Ra. By using Pvu II, a restriction enzyme that cleaves IS 6110 once, and by probing for an IS6110 specific target sequence located to the right of the Pvu II site, we found that the strains H37Rv and H37Ra share 13 IS6110-positive restriction fragments and that one IS6110-positive restriction fragment of H37Rv is replaced by four novel fragments in H37Ra; by probing for an IS6110-specific target sequence to the left of the Pvu II site, 13 shared restriction fragments and 2 differential bands in strain H37Ra were detected. These findings demonstrate that novel insertions of the IS6110 element exist in the avirulent strain H37Ra and raise the question of the role, if any, of IS6110-insertional mutagenesis in the establishment of the avirulent M. tuberculosis H37Ra phenotype.     

Identification of one insertion site of IS6110 in Mycobacterium tuberculosis H37Ra and analysis of the RvD2 deletion in M. tuberculosis clinical isolates

Mycobacterium tuberculosis H37Rv and the attenuated strain H37Ra were used as a model to investigate the virulence properties of M. tuberculosis at the genetic level. To test whether transposition of the insertion element IS6110 might be involved in the loss of virulence of strain H37Ra, the nucleotide sequence of a differential IS6110-positive restriction fragment detected in strain H37Ra, but not in strain H37Rv, was determined. The region flanking the 3' end of the IS6110 element showed partial sequence homology with internal sequences of M. tuberculosis H37Rv genes plcA, plcB and plcC, each one coding for phospholipase C, a well-known bacterial virulence factor. A 100% homology was found between the IS6110-flanking region and an internal sequence of M. bovis plcD, a further phospholipase C gene that is truncated and partly lost in strain H37Rv in the so-called RvD2 deletion. This result indicates that the differential restriction fragment of strain H37Ra originally stems from the plcD gene interrupted by the insertion of the IS6110 element. The occurrence of the RvD2 deletion was then investigated in 45 clinical isolates of M. tuberculosis by Southern blot. The deletion was demonstrated in 15 isolates; the entire RvD2 region (including the undisrupted plcD gene) was detected in 29 isolates, whereas only one isolate showed the RvD2 region in which the plcD gene was interrupted by an IS6110 insertion. It is concluded that disruption of the plcD gene and deletion of the RvD2 region by IS6110 insertion have no consequence for the virulence of M. tuberculosis, although the role of phospholipase C as a virulence factor of M. tuberculosis remains debatable.     

Molecular characterization of Mycobacterium tuberculosis H37Rv/Ra variants: distinguishing the mycobacterial laboratory strain

The Mycobacterium tuberculosis strains H37Rv and H37Ra are the most commonly used controls for M. tuberculosis identification in the clinical and research laboratory setting. To reduce the likelihood of misidentification and possible cross-contamination with this laboratory neotype, it is important to be able to distinguish H37 from clinical isolates. To provide a reference for identifying H37, we used multiple molecular techniques to characterize H37 strains, including 18 of the most frequently used variants available through the American Type Culture Collection. Isolates were genotyped using gene probes to IS6110 and IS1085. In addition, we performed polymorphic GC-rich sequence typing (PGRS), spoligotyping, determination of variable number of tandem repeats (VNTR), and PCR amplification of the mtp40, msx4, and mpp8 polymorphic regions. Southern hybridization with IS6110 provided the most discrimination, differentiating the 18 H37 isolates into 10 discrete patterns made up of 9 H37Rv variants and 1 H37Ra variant. PGRS, IS1085, mpp8, and spoligotyping were not able to distinguish any H37 variants, while VNTR and msx4 discriminated two. Only IS6110 and spoligotyping could distinguish the H37 strain from clinical isolates. In summary, spoligotyping and IS6110 provide a rapid and accurate way to identify H37 contamination, though IS6110 can, in addition, classify many of the H37 variants that would otherwise require phenotypic segregation.     

Identification of genes differentially expressed inMycobacterium tuberculosisby differential display PCR

RNA arbitrarily-primed differential display PCR (RAP-PCR) was used to identify and isolate genes differentially expressed between attenuated (H37Ra) and virulent (H37Rv, Erdman) laboratory strains ofMycobacterium tuberculosis (Mtb). Using this method, cDNA fragments showing homology to three known mycobacterial genes and six putative novel genes in mycobacterial cosmid vectors were identified. Among the putative novelMtbgenes identified, we found: (1) gene MTV041.29, containing multiple tandem repetitive sequences and encoding a putative Gly-, Ala, Asn-rich protein (PPE family); (2) gene MTV004.03, containing the AT10S repetitive gene sequence; (3) gene MTV028.09, encoding a hypothetical protein of unknown function; (4) genes MTCY78.20,21, possibly encoding two hypothetical proteins of unknown function; (5) gene MTCY01A6.09, encoding a putative novel ferrodoxin dependent glutamate synthase; and (6) gene MTCY31.20, encoding a putative cyclohexanone monooxygenase. Using gene specific primers in a second differential display PCR and by RT-PCR amplification, novel genes 1, 2, 3 and 4 were shown to be differentially up-regulated in the attenuatedMtbstrain H37Ra compared to H37Rv and Erdman strain. Overall, we demonstrated that RAP-PCR, as a first step, is a quick and sensitive method for the identification and isolation of novel genes expressed inMtb. Because of limitations inherent to the lack of specificity of arbitrary primers in the RAP-PCR method, a second differential display PCR and RT-PCR amplification with gene-specific primers was necessary in order to confirm differential expression of the identified genes.